Medical examiner reports. Cook County, Illinois

Setting working directory

library(dplyr)
setwd("c:/Users/Ali/Desktop/Medical Examiner/")

read the dataset

medical_examiner <- read.csv("Medical_Examiner_Case_Archive.csv",encoding = "UTF-8")
medical_examiner

Selecting those varibles that are needed

medical_examiner_selected <- medical_examiner %>% select(Case.Number,Date.of.Incident,Date.of.Death,Age,Gender,Race,Latino,Manner.of.Death,Primary.Cause,Incident.Address,Incident.City,longitude,latitude,OBJECTID)
medical_examiner_selected

Select only completed cases

medical_examiner_selected_complete <- medical_examiner_selected[medical_examiner_selected %>% complete.cases(),]
medical_examiner_selected_complete

Cleaning data from outliers, any latitude and longitude > 3*standard deviation

#cleaning data from outliers, any latitude and longitude > 3*standard deviation 
medical_examiner_selected_complete_rmoutlier <- medical_examiner_selected_complete %>% filter(longitude>mean(longitude)-3*sd(longitude) & latitude>mean(latitude)-3*sd(latitude) & longitude<mean(longitude)+3*sd(longitude) & latitude < mean(latitude)+3*(latitude))
medical_examiner_selected_complete_rmoutlier

Creating countour plot for Accident deaths

library("leaflet")
library("data.table")
library("sp")
library("rgdal")
# library("maptools")
library("KernSmooth")
plotdata <- medical_examiner_selected_complete_rmoutlier %>% filter(Manner.of.Death=='NATURAL')
kde <- bkde2D(cbind(plotdata$longitude,plotdata$latitude),bandwidth=c(0.002,0.002),gridsize = c(20,20))

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

CL <- contourLines(kde$x1 , kde$x2 , kde$fhat)
## EXTRACT CONTOUR LINE LEVELS
LEVS <- as.factor(sapply(CL, `[[`, "level"))
NLEV <- length(levels(LEVS))
## CONVERT CONTOUR LINES TO POLYGONS
pgons <- lapply(1:length(CL), function(i)
    Polygons(list(Polygon(cbind(CL[[i]]$x, CL[[i]]$y))), ID=i))
spgons = SpatialPolygons(pgons)
## Leaflet map with polygons
leaflet(spgons) %>% addTiles() %>% 
    addPolygons(color = heat.colors(NLEV, NULL)[LEVS])

## Leaflet map with points and polygons
## Note, this shows some problems with the KDE, in my opinion...
## For example there seems to be a hot spot at the intersection of Mayfield and
## Fillmore, but it's not getting picked up.  Maybe a smaller bw is a good idea?
leaflet(spgons) %>% addTiles() %>%
    addPolygons(color = heat.colors(NLEV, NULL)[LEVS]) %>%
    addCircles(lng = plotdata$longitude, lat = plotdata$latitude,
               radius = .5, opacity = .2, col = "blue")

Creating countour plot for homicide deaths

plotdata <- medical_examiner_selected_complete_rmoutlier %>% filter(Manner.of.Death=='HOMICIDE')
kde <- bkde2D(cbind(plotdata$longitude,plotdata$latitude),bandwidth=c(0.002,0.002),gridsize = c(20,20))

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

CL <- contourLines(kde$x1 , kde$x2 , kde$fhat)
## EXTRACT CONTOUR LINE LEVELS
LEVS <- as.factor(sapply(CL, `[[`, "level"))
NLEV <- length(levels(LEVS))
## CONVERT CONTOUR LINES TO POLYGONS
pgons <- lapply(1:length(CL), function(i)
    Polygons(list(Polygon(cbind(CL[[i]]$x, CL[[i]]$y))), ID=i))
spgons = SpatialPolygons(pgons)
## Leaflet map with polygons
leaflet(spgons) %>% addTiles() %>% 
    addPolygons(color = heat.colors(NLEV, NULL)[LEVS])

Creating countour plot for deaths by suicide

library(leaflet)
plotdata <- medical_examiner_selected_complete_rmoutlier %>% filter(Manner.of.Death=='SUICIDE')
kde <- bkde2D(cbind(plotdata$longitude,plotdata$latitude),bandwidth=c(0.002,0.002),gridsize = c(20,20))

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

CL <- contourLines(kde$x1 , kde$x2 , kde$fhat)
## EXTRACT CONTOUR LINE LEVELS
LEVS <- as.factor(sapply(CL, `[[`, "level"))
NLEV <- length(levels(LEVS))
## CONVERT CONTOUR LINES TO POLYGONS
pgons <- lapply(1:length(CL), function(i)
    Polygons(list(Polygon(cbind(CL[[i]]$x, CL[[i]]$y))), ID=i))
spgons = SpatialPolygons(pgons)
## Leaflet map with polygons
leaflet(spgons) %>% addTiles() %>% 
    addPolygons(color = heat.colors(NLEV, NULL)[LEVS])